panelcn.mops

panelcn.mops detects copy-number variations (CNVs) in targeted next-generation sequencing (NGS) panel data to identify ROI-level and gene-level copy-number changes.

Key Features:

• Accuracy: Demonstrated superior performance compared to five state-of-the-art CNV detection methods in a comparative study of 180 samples.
• Detection Range: Reliably identifies CNVs ranging from partial regions of interest (ROIs) to entire genes encompassing all ROIs.
• Incidental Findings Management: Analyzes reads from the entirety of the panel's ROIs while reporting results only for user-selected genes to limit incidental findings.
• Quality Control: Implements QC criteria at both the sample level and individual ROI level.
• cn.mops Foundation: Built as an extension of the cn.mops package tailored for targeted NGS panels.

Scientific Applications:

• Clinical diagnostics: Detection of CNVs in targeted NGS panels for diagnostic testing.
• Combined variant analysis: Used alongside detection of single-nucleotide variants (SNVs) and small insertions/deletions (indels) to provide comprehensive variant profiling.

Methodology:

Implemented as an extension of cn.mops that analyzes reads from all panel ROIs, applies QC at sample and ROI levels, and reports CNV calls limited to user-selected genes.